Crystal structures of the methane monooxygenase hydroxylase component were solved with a variety of small molecule substrate analogs to probe the role of hydrophobic cavities in facilitating access of substrates to the buried active site. Consistent with the hypothesis that these cavities are important in that regard, the substrate analogs dibromomethane, iodomethane, and iodoethane were found to bind in these cavities. The structure of an additional crystal form of the hydroxylase in the reduced Fe(II)Fe(II) state revealed a previously unobserved mode of carboxylate ligation to the iron atoms. This geometry resembled that of other dinuclear iron enzymes in the reduced state.